Align Hydroxyacylglutathione hydrolase GloC; EC 3.1.2.6; Accessory type II glyoxalase; Glyoxalase II 2; GlxII-2 (uncharacterized)
to candidate GFF1751 Psest_1789 Zn-dependent hydrolases, including glyoxylases
Query= curated2:Q57544 (212 letters) >FitnessBrowser__psRCH2:GFF1751 Length = 287 Score = 68.2 bits (165), Expect = 1e-16 Identities = 59/177 (33%), Positives = 82/177 (46%), Gaps = 20/177 (11%) Query: 34 AERLIQRIEELDLNLKVLLLTHGHLDHVGAAMQLKQHFGVEIWGSNE----KDKF--LFE 87 AERL+ + L ++ LL TH H DH+ AA LKQ G + + +D F LF Sbjct: 49 AERLVDYVRAQGLTVQWLLETHVHADHLSAAPYLKQQLGGRLAIGDRITVVQDTFGKLFN 108 Query: 88 SLPEQAQRFGLPNIDAFLPDRWFNQEGEILKLDGFNFEILHLPGHTPGHIGFIEHEKKVA 147 + E A D D F+ +G+ ++ +H PGHTP + ++ + A Sbjct: 109 AGSEFA-------TDGRQFDHLFH-DGDTFQVGNIQAHAIHTPGHTPACMTYVIGD--AA 158 Query: 148 FTGDVLFQG--GIGRTDFPRGDYETLISSIRTKLLPLNDDIIIIAGHGSYTTIGQEK 202 F GD LF G R DFP GD TL SI+ KL L D + H Y G+E+ Sbjct: 159 FVGDTLFMPDYGTARCDFPGGDARTLYQSIQ-KLFTLPDSTRVFMCH-DYKAPGREE 213 Lambda K H 0.321 0.142 0.430 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 172 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 212 Length of database: 287 Length adjustment: 24 Effective length of query: 188 Effective length of database: 263 Effective search space: 49444 Effective search space used: 49444 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory